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Title

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1		-Widget 3D
	1	+Widget 3D Head

Author

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1		-XWiki.ldomide
	1	+XWiki.paulapopa

Content

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1		-TODO
2		-! pip install -i tvb-widgets
3		-from tvbwidgets.api import SurfaceWidget
4		-from IPython.core.display_functions import display
5		-w3d = SurfaceWidget(...)
6		-display(w3d)
7		-
8		-{{html}}<iframe src=" https://drive.google.com/file/d/1PXsxLqydNDDORIK85cQaEgGt9QdWLcC7/preview" width="840" height="480" allow="autoplay"></iframe>{{/html}}
	1	+Source code: [[https:~~/~~/github.com/the-virtual-brain/tvb-widgets>>https://github.com/the-virtual-brain/tvb-widgets]]
	2	+
	3	+Immediate testing: [[https:~~/~~/lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/TVB%20Widgets/REPO/tvb-widgets/notebooks/HeadWidget.ipynb>>https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/TVB%20Widgets/REPO/tvb-widgets/notebooks/HeadWidget.ipynb]]
	4	+
	5	+== Purpose ==
	6	+
	7	+It is a Jupyter widget intended for visualization of the 3D Head data available for a patient:
	8	+
	9	+* surfaces of different types (cortex, face, skull, etc)
	10	+* connectivity region centers
	11	+* sensors locations (SEEG, MEG, EEG)
	12	+
	13	+== Inputs ==
	14	+
	15	+It supports the above data in the form of their corresponding TVB datatypes:
	16	+
	17	+* Surface (CorticalSurface, FaceSurface, etc)
	18	+* Connectivity
	19	+* Sensors (SensorsInternal, SensorsMEG, SensorsEEG)
	20	+
	21	+== Installation ==
	22	+
	23	+(% class="box" %)
	24	+(((
	25	+pip install tvb-widgets
	26	+)))
	27	+
	28	+== API usage ==
	29	+
	30	+We need to first import the widget __API from tvbwidgets__// //package, together with the __TVB API __and the __display__ function:
	31	+
	32	+(% class="box" %)
	33	+(((
	34	+import tvbwidgets.api as api
	35	+
	36	+from tvb.simulator.lab import *
	37	+
	38	+from IPython.core.display_functions import display
	39	+)))
	40	+
	41	+Then, there are 2 options to work with the widget:
	42	+
	43	+1. Use a file browser to load the data and automatically display it
	44	+1. Use directly the API to load the data and display it
	45	+
	46	+
	47	+For the first option, you have to run the following 2 lines of code in a notebook cell and then just use the UI controls:
	48	+
	49	+(% class="box" %)
	50	+(((
	51	+widget = api.HeadBrowser()
	52	+display(widget)
	53	+)))
	54	+
	55	+{{html}}
	56	+<iframe src="https://drive.google.com/file/d/1lY3X5eqJfOLmkmHuBa2iq_Aas8mDPa1e/preview" width="840" height="480" allow="autoplay"></iframe>
	57	+{{/html}}
	58	+
	59	+
	60	+For the second option, the API is described below:
	61	+
	62	+In a new cell, we instantiate the **HeadWidget** and a **FaceSurface** datatype that we want to visualize. Using the //**add_datatype**// method we add the surface to our widget and __display__ the widget:
	63	+
	64	+(% class="box" %)
	65	+(((
	66	+widget = api.HeadWidget()
	67	+
	68	+face = surfaces.FaceSurface().from_file()
	69	+
	70	+face.configure()
	71	+
	72	+widget.add_datatype(face)
	73	+display(widget)
	74	+)))
	75	+
	76	+{{html}}
	77	+<iframe src="https://drive.google.com/file/d/1Egp9Lk-HGMATc9em6Kw_jSHmybTD2vzM/preview" width="840" height="480" allow="autoplay"></iframe>
	78	+{{/html}}
	79	+
	80	+Next, we can continue adding other datatypes to this widget, by calling //**add_datatype**// multiple times. A maximum of 10 datatypes are supported by this widget.
	81	+
	82	+The **Config** object can be used to tweak the display options for each datatype.
	83	+
	84	+In the code below, we add a **Connectivity** and SEEG **Sensors:**
	85	+
	86	+(% class="box" %)
	87	+(((
	88	+conn = connectivity.Connectivity().from_file()
	89	+
	90	+conn.configure()
	91	+
	92	+widget.add_datatype(conn)
	93	+
	94	+
	95	+seeg = sensors.SensorsInternal().from_file()
	96	+
	97	+seeg.configure()
	98	+
	99	+widget.add_datatype(seeg, api.HeadWidgetConfig(name='SEEG'))
	100	+)))
	101	+
	102	+{{html}}
	103	+<iframe src="https://drive.google.com/file/d/1RLwts75Hh31LoPdWLK7QOM61KIsOabF1/preview" width="840" height="480" allow="autoplay"></iframe>
	104	+{{/html}}
	105	+
	106	+We can also provide a **RegionMapping** to be used as colormap for a surface:
	107	+
	108	+(% class="box" %)
	109	+(((
	110	+reg_map = region_mapping.RegionMapping.from_file()
	111	+
	112	+config = api.HeadWidgetConfig(name='Cortex')
	113	+
	114	+config.add_region_mapping_as_cmap(reg_map)
	115	+
	116	+
	117	+cortex = surfaces.CorticalSurface().from_file()
	118	+
	119	+cortex.configure()
	120	+
	121	+
	122	+widget = api.HeadWidget()
	123	+
	124	+widget.add_datatype(cortex, config)
	125	+
	126	+display(widget)
	127	+)))
	128	+
	129	+{{html}}
	130	+<iframe src="https://drive.google.com/file/d/1zrbjdb8Y4V5rqg7Y7LDGlHHMS0RH8luz/preview" width="840" height="480" allow="autoplay"></iframe>
	131	+{{/html}}